X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 291.15
Details 0.1 M BICINE, 10%(w/v) PEG 6000, pH 9.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 111.11 α = 90
b = 133.5 β = 90
c = 169.07 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M-F -- 2015-12-14
Diffraction Radiation
Monochromator Protocol
Si (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.9790 ESRF ID23-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3 49.08 100.0 0.219 -- -- 13.3 -- 51096 -- -- 89.21
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.0 3.09 100.0 2.78 -- -- 27.8 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 3.0 49.08 -- 1.34 -- 51018 2647 99.97 -- 0.2381 0.2369 0.2585 RANDOM SELECTION
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.0 3.0546 -- 142 2479 0.3847 0.4375 -- 100.0
X Ray Diffraction 3.0546 3.1133 -- 127 2540 0.3671 0.4103 -- 100.0
X Ray Diffraction 3.1133 3.1769 -- 141 2522 0.3424 0.365 -- 100.0
X Ray Diffraction 3.1769 3.2459 -- 140 2504 0.3373 0.3844 -- 100.0
X Ray Diffraction 3.2459 3.3214 -- 152 2510 0.3221 0.3573 -- 100.0
X Ray Diffraction 3.3214 3.4045 -- 134 2502 0.3008 0.3808 -- 100.0
X Ray Diffraction 3.4045 3.4965 -- 150 2501 0.2861 0.308 -- 100.0
X Ray Diffraction 3.4965 3.5993 -- 144 2537 0.2707 0.2807 -- 100.0
X Ray Diffraction 3.5993 3.7155 -- 151 2513 0.2777 0.2942 -- 100.0
X Ray Diffraction 3.7155 3.8482 -- 128 2530 0.2508 0.314 -- 100.0
X Ray Diffraction 3.8482 4.0022 -- 130 2532 0.2322 0.3023 -- 100.0
X Ray Diffraction 4.0022 4.1843 -- 138 2536 0.2152 0.2427 -- 100.0
X Ray Diffraction 4.1843 4.4048 -- 141 2543 0.2062 0.2212 -- 100.0
X Ray Diffraction 4.4048 4.6805 -- 132 2561 0.2007 0.1944 -- 100.0
X Ray Diffraction 4.6805 5.0416 -- 144 2547 0.1898 0.1874 -- 100.0
X Ray Diffraction 5.0416 5.5483 -- 138 2569 0.2128 0.2303 -- 100.0
X Ray Diffraction 5.5483 6.3497 -- 121 2608 0.2235 0.263 -- 100.0
X Ray Diffraction 6.3497 7.9944 -- 129 2631 0.2242 0.2091 -- 100.0
X Ray Diffraction 7.9944 49.087 -- 165 2706 0.2153 0.2323 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 79.4318
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 15.276
f_chiral_restr 0.043
f_bond_d 0.003
f_angle_d 0.543
f_plane_restr 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10657
Nucleic Acid Atoms 0
Heterogen Atoms 24
Solvent Atoms 0

Software

Software
Software Name Purpose
Aimless data scaling version: 0.5.17
PHENIX refinement version: 1.10_2152
PDB_EXTRACT data extraction version: 3.20
XDS data reduction version: Oct 15, 2015
PHENIX phasing version: 1.10-2152
PHENIX model building version: 1.10-2152
Coot model building version: 0.8-pre (revision 4727)